Abstract 6763: Spatial profiling of cancer-associated fibroblasts in non-small cell lung cancer
Authors: Yunhe Liu, Guangchun Han, Enyu Dai, Guangsheng Pei, Jiahui Jiang, Humam Kadara, Linghua Wang
Journal: Cancer Research (2023)

Abstract Cancer-associated fibroblast (CAF) is an unique component of the tumor microenviroment (TME). CAFs heterogeneous have been identified by recent single-cell studies. However, their spatial distribution, orgnization patterns and neighbors remain incompletely understood. Deep profiling of CAFs in tissue context may provides new insights into improved understanding of their functions and identify targets for the development of CAF-targeted therapies.We obtained the open-source CosMx SMI dataset generated on 8 tissue sections from 5 non-small-cell lung cancer (NSCLC) tissues (He, S. et al. Nat Biotechnol. 2022). We extracted the cells’ spatial locations and transcriptome data for subsequent analyses. Quanlity filtering, data normalization, batch correction and clustering analysis was performed by Seurat package. Cell type was defined based on canonical immune markers and curated gene sets. In addition, we applied NMF clustering approach to define the spatial subtypes of CAFs based on the composition of neighboring cells. After that, Four spatial subtypes of CAFs were defined, exhibiting distinct spatial distribution patterns and compositions of neiboring cells, including CAFs that are clustered with tumor cells, CAFs localized within stromal, CAFs co-localized with B cells and T cells within the tertiary lymphoid structures, and CAFs localized within myeloid-enriched areas. Notably, we observed an intimate link between their spatial location and tarnscriptioanl states, i.e., these different spatial CAF subtypes showed clearly distinct expression profiles, may suggest their heterogeneous functions in the tumor microenviroment. For example, tumor-enriched CAFs showed high expression of contractile (e.g., ACTA2, TAGLN) and extracellular matrix (COL1A1) related genes, resembling myofibroblast (myCAFs), whereas the TLS-niches CAFs showed high expression of genes involved in antigen presentation such as major histocompatibility complex class II molecules and CD74, suggesting their antigen presentation function and were identified as apCAFs. Consistently, we observed high expression of inflammation related genes such as interleukin and PDGFRA in the myeloid-enriched CAFs suggesting an inflammatory phenotype (iCAFs). In addition, these CAFs in different spatial subtypes showed differential expression of molecular pathways regulating stress and inflammation response, likely reflecting their complex interactions with other components of the tunmor microenvironment. We also included single-cell RNA sequencing (scRNA-seq) and spatially resolved whole transcriptomics datasets for cross validation of our novel discoveries in additional cohorts.In summary, by applying a novel approach to classify CAFs in the spatial context, this study provided novel insights into an improved understanding of the phenotypic and functional heterogeneity of CAFs in the tunmor microenvironment of NSCLC. Citation Format: Yunhe Liu, Guangchun Han, Enyu Dai, Guangsheng Pei, Jiahui Jiang, Humam Kadara, Linghua Wang. Spatial profiling of cancer-associated fibroblasts in non-small cell lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6763.